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| Status |
Public on Feb 23, 2024 |
| Title |
ChIP,4do,chl27,ChIP,Rep3 |
| Sample type |
SRA |
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| Source name |
Seedling
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Seedling
cell line: chl27
cell type: Chloroplast
genotype: wild type
treatment: none
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| Growth protocol |
Seeds were stratified in darkness at 4ºC for 48 hours, and for fourteen days-old plants, they grown on soil at 22ºC under white LED light (100 umol m-2 s-1) in 16h/8h day/night Cycle. For four days-old plants they were grown on 0.5X MS plates under continuous light (100 umol m-2 s-1).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fifty 4-5 days-old seedlings were harvested, crosslinked with 4 % formaldehyde for 4 hours, and homogenized in chloroplast enrichment buffer (0.33 M Sorbitol, 30 mM HEPES-KOH (pH 7.5), 0.001% beta-mercaptoethanol) using a pestle. The homogenate was filtered through two layers of miracloth, and centrifuged at 1500 g for 5 minutes at 4ºC. The pelleted chloroplasts were resuspended in 1 ml of chloroplast enrichment buffer.
Sequencing libraries were prepared as reported (Bowman, et al. 2013, BMC Genomics, 14:466).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Reads were adapter trimmed using Trim-galore v0.4.1
Mapping was performed using Bowtie2 v2.2.8.9 with normal paired reads and no errors were allowed
Read counts on defined genomic regions were determined using bedtools v.2.25.0
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Genome coverage per nucleotide is included for all the datasets in txt format
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| Submission date |
Feb 22, 2024 |
| Last update date |
Feb 23, 2024 |
| Contact name |
V Miguel Palomar |
| E-mail(s) |
vpalomar@umich.edu
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| Phone |
7342195985
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| Organization name |
University of Michigan
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| Department |
MCDB
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| Lab |
Wierzbicki
|
| Street address |
1105 N. University Ave.
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platform ID |
GPL26208 |
| Series (2) |
| GSE228226 |
Chloroplast nucleoid is organized by membrane association of transcribed genes [ChIP] |
| GSE228230 |
Chloroplast nucleoid is organized by membrane association of transcribed genes |
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| Relations |
| BioSample |
SAMN40038511 |
| SRA |
SRX23703327 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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